Evolving Spectrum of Adenosine Deaminase Deficiency: Assessing Genotype Pathogenicity Based on Expressed ADA Activity of 46 Variants

Background Deficiency of adenosine deaminase 1 (ADA) has broad clinical and genetic heterogeneity. Screening techniques can identify asymptomatic infants whose phenotype and prognosis are indeterminate, and who may carry ADA variants of unknown significance. Objective To systematically assess the pathogenic potential of rare ADA missense variants, and to better define the relationship of red cell deoxyadenosine nucleotide (dAXP) content to phenotype. Methods We expressed 46 ADA missense variants in the ADA-deficient SØ3834 strain of E. coli and defined Genotype Categories (GC) ranked I - IV by increasing expressed ADA activity. We assessed relationships among GC rank, red cell dAXP, and phenotype in 58 reference patients with 50 different genotypes. We used our GC ranking system to benchmark AlphaMissense for predicting variant pathogenicity, and a minigene assay to identify an exonic splicing variant in ADA exon 9. Results The 46 missense variants expressed ∼0.001% to ∼70% of WT ADA activity (40% had <0.05% of WT ADA activity and 50% expressed >1%). Red cell dAXP ranged from undetectable to >75% of total adenine nucleotides and correlated well with phenotype. Both red cell dAXP and clinical severity were inversely related to “txADA” (total ADA activity expressed by both inherited variants). Our GC scoring system performed better than AlphaMissense in assessing variant pathogenicity, particularly for less deleterious variants. Conclusion For ADA deficiency, pathogenicity is a continuum and conditional, depending on the total ADA activity contributed by both inherited variants as indicated by GC rank. However, in patients with indeterminate phenotype identified by screening, red cell dAXP measured at diagnosis may have greater prognostic value than GC rank .